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LOC129994470 ATAC-STARR-seq lymphoblastoid active region 22998 [ Homo sapiens (human) ]

Gene ID: 129994470, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129994470
Gene description
ATAC-STARR-seq lymphoblastoid active region 22998
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence represents an accessible chromatin region that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC129994470 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (122775234..122775363)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (123292065..123292194)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (122110929..122111058)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927357 Neighboring gene long intergenic non-protein coding RNA 2201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22997 Neighboring gene arginine-fifty homeobox pseudogene 1 Neighboring gene MPRA-validated peak5446 silencer Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:122087198-122087764 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22999 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23001 Neighboring gene uncharacterized LOC105379154 Neighboring gene uncharacterized LOC124901216 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:122145340-122145844 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:122145845-122146350 Neighboring gene sorting nexin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16270 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16271 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:122195290-122196259 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:122196439-122196653 Neighboring gene Sharpr-MPRA regulatory region 12893 Neighboring gene sorting nexin 24 Neighboring gene MPRA-validated peak5448 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23002 Neighboring gene small nucleolar RNA U13

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_173916.1 

    Range
    101..230
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    122775234..122775363
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    123292065..123292194
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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